This quick-start tutorial will guide you through using the provided data files to recreate a normalization, plotting and differential expression analysis.
A set of example files for use with this tutorial can be found at; https://drive.google.com/drive/folders/1FocRZ6x05_0TwC_xiSIYwhsj9KAYNZwZ?usp=sharing
Download and save the following files:
- GENAVi_Cell_Line_RNA_seq_count_matrix.csv
- GENAVi_Cell_Line_RNA_seq_metadata.csv
- GENAVi_gene_list_input.txt
Open junkdnalab.shinyapps.io/GENAVi/
In the ‘Gene Expression’ tab of GENAVi, select the ‘Data upload’ button to bring up a separate menu then select the ‘Browse’ button to upload your count matrix.

- Select the ‘Visualization’ tab, and then the ‘Clustering Plots’ sub tab. By default, Figure 3 from the Vignette will be created, showing the clustering of all samples by all genes shown in the data table.

- To plot the expression of individual genes as bar charts select the appropriate normalization method (a detailed explanation of which normalization method is suited to different data types is available in the Vignette). Variance stabilization transformation is optimal for most datasets for this purpose. Search and select the gene of interest in the data table. Once selected move to the ‘Visualization’ tab, and the ‘Expression plots’ sub-tab.


- To perform DEA select the ‘Differential Expression Analysis’ tab. Select ‘Metadata upload’ to bring up a separate menu then select the ‘Browse’ button to upload the metadata file, which will be displayed in the app.
